Running BF on pavement only on a periodic basis cause it. I did three miles yesterday with a few hundred yards of Florida hot black top every half mile. I also got some blisters. However, my skin is thick enough that they are not going to rupture. Shoes for the next run or two or I run on grass/dirt BF. Anyone can get blisters if they change the conditions they run under.

I recommend running while your feet are still blistered. Then you will be forced to NOT do whatever it is that is causing the blister. I have never had a blister since running on blistered feet...shod or otherwise.

It's difficult to guess at the exact cause without seeing your run. One possibility is that you just haven't done enough barefooting to toughen your skin. Another is that you're not pulling your foot backward slightly before contact. Lifting your toes slightly before contact may help. However the fact that it's behind the 2nd toe suggests you're not distributing your weight well across the foot. Edward Yu's book has Feldenkrais lessons which show you how to coordinate your entire body so that your power is directed to the lever of your big toe. This helped me to solve a problem I had with 2nd metatarsal pain.

I, too, have struggled with blisters, but I only have issues when it's really too cold (<40 deg. F) or the surface temp is too hot for me. If the sun is blazing outside, I have to be wary even if I'm running on smooth sidewalk or pavement. I have zero issues at the shaded trail at the park in town, so I know it's not simply about the outside temp. Not sure if this is the case with everyone or not.

Also, people with Morton's toe (2nd toe longest) tend to have blistering issues at the 2nd metatarsal head - where is sounds like your issues lie. My blisters there dissipated as I got more experience (read: better form) and thicker pads. Hope this helps!